minor fixes for setting configs etc

Added Mosquito bands and P/Q recognition to 'flat chromosome end' if-block
added links
fixed SGD genes
TSV keep reference in box display
TSV keep reference in box display
TSV keep reference in box display
TSV keep reference in box display
fixed variation legend in ldview
added hollow boxes wehre alelle = ref
added Source=Sanger to resequencing coverage
fixed the Collapse display
changed text for blank snps
now snp legend only shows the types of SNPs in the display plus the negative snp grey box
rm strain from text
rm 'consequence' or changed word to 'type'
rm compare to from link
added SARA SNPs
new status for some vega genes
fixed the display of the left arrowed triangles